Nonradical mechanism of (bi)sulfite reaction with DEPMPO: cautionary note for SO3*- radical spin trapping

Knowledge of the formation of radicals from sulfites, in vivo, is of interest in understanding the allergic and inflammatory responses to environmental sulfur dioxide exposure. Sulfite anion trioxide (SO(3)(-*)) radical formation was measured in mice, preloaded with the spin trap, 5-(diethoxy-phosphoryl)-5-methyl-pyrrolidine-N-oxide, (DEPMPO). Based on spin trapping NMR, a surprising quantity of reduced SO(3)(-*)-adduct was observed that did not depend on co-administration of oxidizing agents, suggesting a possible nonradical reaction between (bi)sulfite and DEPMPO. The products of the reversible nucleophylic addition of (bi)sulfite to the nitrone functional group were identified using (31)P-NMR, (1)H-NMR, and (13)C-NMR spectroscopy as cis- and trans- stereoisomers of hydroxylamine and confirmed by quantum chemical calculations. Oxidation of the hydroxylamines results in the formation of two corresponding cis- and trans-isomeric nitroxides, only one of which has been earlier described as the paramagnetic adduct of genuinely trapped SO(3)(-*) radical. The results demonstrate that SO(3)(-*) detection using nitrone spin traps such as DEPMPO and DMPO may involve nonradical addition reactions except in cases when the required controls unambiguously prove a radical mechanism.     

Small heat shock protein Hsp27 prevents heat-induced aggregation of F-actin by forming soluble complexes with denatured actin

Previously, we have shown that the small heat shock protein with apparent molecular mass 27 kDa (Hsp27) does not affect the thermal unfolding of F-actin, but effectively prevents aggregation of thermally denatured F-actin [Pivovarova AV, Mikhailova VV, Chernik IS, Chebotareva NA, Levitsky DI & Gusev NB (2005) Biochem Biophys Res Commun331, 1548-1553], and supposed that Hsp27 prevents heat-induced aggregation of F-actin by forming soluble complexes with denatured actin. In the present work, we applied dynamic light scattering, analytical ultracentrifugation and size exclusion chromatography to examine the properties of complexes formed by denatured actin with a recombinant human Hsp27 mutant (Hsp27-3D) mimicking the naturally occurring phosphorylation of this protein at Ser15, Ser78, and Ser82. Our results show that formation of these complexes occurs upon heating and accompanies the F-actin thermal denaturation. All the methods show that the size of actin-Hsp27-3D complexes decreases with increasing Hsp27-3D concentration in the incubation mixture and that saturation occurs at approximately equimolar concentrations of Hsp27-3D and actin. Under these conditions, the complexes exhibit a hydrodynamic radius of approximately 16 nm, a sedimentation coefficient of 17-20 S, and a molecular mass of about 2 MDa. It is supposed that Hsp27-3D binds to denatured actin monomers or short oligomers dissociated from actin filaments upon heating and protects them from aggregation by forming relatively small and highly soluble complexes. This mechanism might explain how small heat shock proteins prevent aggregation of denatured actin and by this means protect the cytoskeleton and the whole cell from damage caused by accumulation of large insoluble aggregates under heat shock conditions.     

New oligonucleotide analogues based on morpholine subunits joined by oxalyl diamide tether

We report on the design, synthesis and some of the properties of the new oligonucleotide analogues based on morpholine nucleoside (MorB) subunits joined by an oxalyl diamide tether instead of a phosphate group. The synthetic strategy and oligomer design are optimized to easily obtain target substances without using protective groups. The dimers HOMorU-Ox-NHMorU, HOMorU-Ox-NHMorA, and uracil containing the hexamer HOMorU-(Ox-NHMorU)5 were synthesized. The structures of all substances were confirmed by 1H, 13C, NMR, and mass spectroscopy. Base stacking interactions in dimers were revealed by CD-spectra data.     

Sodium Ions as Regulators of Transcription in Mammalian Cells

Biochemistry (Moscow) - The maintenance of an uneven distribution of Na+ and K+ ions between the cytoplasm and extracellular medium is the basis for the functioning of any animal cell. Changes in...     

ClusPro: performance in CAPRI rounds 6-11 and the new server

ClusPro is the first fully automated, web-based program for docking protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures. The server performs rigid body docking, energy screening, and clustering to produce models. The program output is a short list of putative complexes ranked according to their clustering properties. ClusPro has been participating in CAPRI since January 2003, submitting predictions within 24 h after a target becomes available. In Rounds 6-11, ClusPro generated acceptable submissions for Targets 22, 25, and 27. In general, acceptable models were obtained for the relatively easy targets without substantial conformational changes upon binding. We also describe the new version of ClusPro that incorporates our recently developed docking program PIPER. PIPER is based on the fast Fourier transform correlation approach, but the method is extended to use pairwise interaction potentials, thereby increasing the number of near-native docked structures.     

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer

Gene coexpression network analysis is a powerful “data-driven” approach essential for understanding cancer biology and mechanisms of tumor development. Yet, despite the completion of thousands of studies on cancer gene expression, there have been few attempts to normalize and integrate co-expression data from scattered sources in a concise “meta-analysis” framework. We generated such a resource by exploring gene coexpression networks in 82 microarray datasets from 9 major human cancer types. The analysis was conducted using an elaborate weighted gene coexpression network (WGCNA) methodology and identified over 3,000 robust gene coexpression modules. The modules covered a range of known tumor features, such as proliferation, extracellular matrix remodeling, hypoxia, inflammation, angiogenesis, tumor differentiation programs, specific signaling pathways, genomic alterations, and biomarkers of individual tumor subtypes. To prioritize genes with respect to those tumor features, we ranked genes within each module by connectivity, leading to identification of module-specific functionally prominent hub genes. To showcase the utility of this network information, we positioned known cancer drug targets within the coexpression networks and predicted that Anakinra, an anti-rheumatoid therapeutic agent, may be promising for development in colorectal cancer. We offer a comprehensive, normalized and well documented collection of >3000 gene coexpression modules in a variety of cancers as a rich data resource to facilitate further progress in cancer research.     

15N-labeling to determine chlorophyll synthesis and degradation in Synechocystis sp. PCC 6803 strains lacking one or both photosystems

Rates of chlorophyll synthesis and degradation were analyzed in Synechocystis sp. PCC 6803 wild type and mutants lacking one or both photosystems by labeling cells with ((15)NH(4))(2)SO(4) and Na(15)NO(3). Pigments extracted from cells were separated by HPLC and incorporation of the (15)N label into porphyrins was subsequently examined by MALDI-TOF mass spectrometry. The life time (tau) of chlorophyll in wild-type Synechocystis grown at a light intensity of 100 micromol photons m(-2) s(-1) was determined to be about 300 h, much longer than the cell doubling time of about 14 h. Slow chlorophyll degradation (tau approximately 200-400 h) was also observed in Photosystem I-less and in Photosystem II-less Synechocystis mutants, whereas in a mutant lacking both Photosystem I and Photosystem II chlorophyll degradation was accelerated 4-5 fold (tau approximately 50 h). Chlorophyllide and pheophorbide were identified as intermediates of chlorophyll degradation in the Photosystem I-less/Photosystem II-less mutant. In comparison with the wild type, the chlorophyll synthesis rate was five-fold slower in the Photosystem I-less strain and about eight-fold slower in the strain lacking both photosystems, resulting in different chlorophyll levels in the various mutants. The results presented in this paper demonstrate the presence of a regulation that adjusts the rate of chlorophyll synthesis according to the needs of chlorophyll-binding polypeptides associated with the photosystems.     

Regulation of the tetrapyrrole biosynthetic pathway leading to heme and chlorophyll in plants and cyanobacteria

Photosynthetic organisms synthesize chlorophylls, hemes, and bilin pigments via a common tetrapyrrole biosynthetic pathway. This review summarizes current knowledge about the regulation of this pathway in plants, algae, and cyanobacteria. Particular emphasis is placed on the regulation of glutamate-1-semialdehyde formation and on the channelling of protoporphyrin IX into the heme and chlorophyll branches. The potential role of chlorophyll molecules that are not bound to photosynthetic pigment-protein complexes ('free chlorophylls') or of other Mg-containing porphyrins in regulation of tetrapyrrole synthesis is also discussed.     

Does Interaction between the Motor and Regulatory Domains of the Myosin Head Occur during ATPase Cycle? Evidence from Thermal Unfolding Studies on Myosin Subfragment 1

Myosin head (myosin subfragment 1, S1) consists of two major structural domains, the motor (or catalytic) domain and the regulatory domain. Functioning of the myosin head as a molecular motor is believed to involve a rotation of the regulatory domain (lever arm) relative to the motor domain during the ATPase cycle. According to predictions, this rotation can be accompanied by an interaction between the motor domain and the C-terminus of the essential light chain (ELC) associated with the regulatory domain. To check this assumption, we applied differential scanning calorimetry (DSC) combined with temperature dependences of fluorescence to study changes in thermal unfolding and the domain structure of S1, which occur upon formation of the ternary complexes S1-ADP-AlF₄^- and S1-ADP-BeF_x that mimic S1 ATPase intermediate states S1**-ADP-P_i and S1*-ATP, respectively. To identify the thermal transitions on the DSC profiles (i.e. to assign them to the structural domains of S1), we compared the DSC data with temperature-induced changes in fluorescence of either tryptophan residues, located only in the motor domain, or recombinant ELC mutants (light chain 1 isoform), which were first fluorescently labeled at different positions in their C-terminal half and then introduced into the S1 regulatory domain. We show that formation of the ternary complexes S1-ADP-AlF₄^- and S1-ADP-BeF_x significantly stabilizes not only the motor domain, but also the regulatory domain of the S1 molecule implying interdomain interaction via ELC. This is consistent with the previously proposed concepts and also adds some new interesting details to the molecular mechanism of the myosin ATPase cycle.